tbuckley/cabot-search huggingface dataset:
SARS-CoV-2, fertility and assisted reproduction
Authors: Baris Ata, Nathalie Vermeulen, Edgar Mocanu, Luca Gianaroli, Kersti Lundin, Satu Rautakallio-Hokkanen, Juha S Tapanainen, Anna Veiga
Journal: Human Reproduction Update (2022)

In 2020, SARS-CoV-2 and the COVID-19 pandemic had a huge impact on the access to and provision of ART treatments. Gradually, knowledge of the virus and its transmission has become available, allowing ART activities to resume. Still, questions on the impact of the virus on human gametes and fertility remain.
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution
Authors: Ruobing Han, Lei Han, Xunwu Zhao, Qianghui Wang, Yanling Xia, Heping Li
Journal: Genomics Proteomics & Bioinformatics (2022)

Abstract Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (RET, PPP2R1A, PPP2R1B, YWHAB, YWHAZ, and RPS6) and positively selected genes (eIF4E, Wnt8A, Wnt9B, BMP4, and TP53) were identified, which could contribute to rapid antler growth without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (Cervus elaphus), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.
Respiratory and Cardiometabolic Comorbidities and Stages I to III NSCLC Survival: A Pooled Analysis From the International Lung Cancer Consortium
Authors: Miguel García-Pardo, Amy Chang, Sabine Schmid, Mei Dong, M. Catherine Brown, David Christiani, Hilary Aurora Tindel, Paul Brennan, Chu Chen, Jie Zhang, Brid M. Ryan, David Zaridze, Matthew B. Schabath, Leticia Ferro Leal, Rui Manuel Reis, Adonina Tardon, Guillermo Fernández-Tardon, Sanjay S. Shete, Angeline Andrew, Hermann Brenner, Wei Xu, Rayjean J. Hung, Geoffrey Liu
Journal: Journal of Thoracic Oncology (2022)
Prediction of Distant Metastases After Stereotactic Body Radiation Therapy for Early Stage NSCLC: Development and External Validation of a Multi-Institutional Model
Authors: Sarah J. Gao, Lan Jin, Hugh W. Meadows, Timothy D. Shafman, Cary P. Gross, James B. Yu, Hugo J.W. L. Aerts, Joseph A. Miccio, John M. Stahl, Raymond H. Mak, Roy H. Decker, Benjamin H. Kann
Journal: Journal of Thoracic Oncology (2022)
Comparison in Retreatments between Bevacizumab and Ranibizumab Intravitreal Injections for Retinopathy of Prematurity
Authors: Nimesh A. Patel, Luis A. Acaba-Berrocal, Sandra Hoyek, Kenneth C. Fan, Maria Ana Martinez-Castellanos, Caroline R. Baumal, C. Armitage Harper, Audina M. Berrocal, Wu Wei-Chi, Rand Spencer, Shunji Kusaka, Polly Quiram, Jose Asilis, Michael P. Blair, Swati Agarwal, Anna Ells, Cagri G. Besirli, Irena Tsui, Thomas C. Lee, Aaron Nagiel, Andres Kychenthal, Jessica Kovarik, Anton Orlin, Janet Alexander, Vaidehi S. Dedania, Sengul Ozdek, Michel J. Shami, Cornelius Regan, Shilpa Desai, Moran Roni Levin, Deborah Y. Chong, Mrinali Gupta, Adam Pflugrath, Ashkan Abbey, Christopher G. Fuller, Lori E. Coors, Nicolas Yannuzzi, Catherine Negron, Hasenin Al-khersan, Paul Runge, Huseyin Baran Ozdemir, Tugce Kucukbalci, Chiharu Iwahashi, Mark Solinski, David Sutter, Jonathan Sears, Christine Sonnie, David Portney, Jake Duker, Tamara Lenis, Andreas Di-Luciano, Pablo Chamartin, Nikisha Kothari, Grecia Yael Ortiz-Ramirez, Gabriela Patricia Amadeo Oreggioni, Ameay V. Naravane, Peter J. Belin, Nahomy Ledesma Vicioso, Demetrios Vavvas, M. Elizabeth Hartnett, Robinson V.P. Chan, Eric Nudleman, Darius M. Moshfeghi, Atchara Amphornphruet, Michael Chiang, Michael J. Shapiro, J. Peter Campbell, Lejla Vajzovic, Mario Capecchi, G. Baker Hubbard, Jason Horowtiz, Rabia Karani, Rosina Negrin Martin, Emmanuel Chang
Journal: Ophthalmology (2022)
Indoor environmental exposures and obstructive lung disease phenotypes among children with asthma living in poor urban neighborhoods
Authors: Torie Grant, Travis Lilley, Meredith C. McCormack, Paul J. Rathouz, Roger Peng, Corinne A. Keet, Ana Rule, Meghan Davis, Susan Balcer-Whaley, Michelle Newman, Elizabeth C. Matsui
Journal: Journal of Allergy and Clinical Immunology (2022)
Reply to “A Commentary on “Personalized pre-habilitation reduces anastomotic complications compared to up front surgery before ileocolic resection in high-risk patients with Crohn's disease: A single center retrospective study” [Int. J. Surg. 105 (2022) 106815]”
Authors: Charlotte Ferrandis, Regis Souche, Thomas Bardol
Journal: International Journal of Surgery (2022)
Abstract 842: Potential Role of MicroRNAs in the Pathogenesis of Diabetic Cardiomyopathy
Authors: Ioannis Karakikes, Andrew Feber, Tony E Godfrey, Roger J Hajjar, Djamel Lebeche
Journal: Circulation (2008)

Cardiac dysfunction is a common and important manifestation of diabetes mellitus and accounts for much of the increased mortality in diabetic patients. Recent studies have uncovered key roles for a family of newly discovered small non-coding regulatory RNA molecules, known as microRNAs (miRNAs), in the control of diverse aspects of cardiac function and dysfunction. However, it remains to be shown whether the expression of miRNAs is altered in the heart in response to diabetes and accounts for the pathogenesis of the disease. We have determined the expression profile of miRNAs in the heart of a rat model of type 2 diabetes using a custom Affymetrix microarray platform in order to gain a better understanding of their possible involvement in diabetic cardiomyopathy. We Identified 17 miRNAs that are differentially regulated during diabetic cardiomyopathy, suggesting that they might function as modulators of this condition. Interestingly, most of the identified miRNAs were similarly dysregulated in type 2 diabetic failing human hearts. Since type 2 diabetes is associated with insulin resistance, we further investigated the functional significance of these miRNAs by over-expression using synthetic miRNA mimics in vitro . Overexpression of a single miRNA (mir-152), which was up-regulated in diabetic cardiomyopathy, inhibited insulin-stimulated glucose uptake and induced cardiac hypertrophy in rat neonatal myocytes. Additionally, mir-152 significantly increased the Phospholamban/Serca2a ratio, suggesting abnormal calcium handling. Our results suggest that specific miRNAs play important roles in myocardial dysfunction associated with insulin resistance and may provide novel therapeutic approaches for the management of diabetes-induced cardiomyopathy.
A multifunctional neuromodulation platform utilizing Schwann cell-derived exosomes orchestrates bone microenvironment via immunomodulation, angiogenesis and osteogenesis
Authors: Zhichao Hao, Lin Ren, Zhen Zhang, Zaiwu Yang, Shujie Wu, Gen Liu, Bin Cheng, Jun Wu, Juan Xia
Journal: Bioactive Materials (2022)

Recent evidence highlights multifaceted biological needs to recapitulate the bone microenvironment for bone regeneration. Neurotization has great potential for realizing multi-system modulations in bone tissue engineering (BTE). However, a neural strategy involving all the key bone repair steps temporally has not yet been reported. In this study, we reported the neural tissue engineering hydrogel-encapsulated Schwann cell-derived exosomes (SC Exo). This sustained-release SC Exo system prominently enhanced bone regeneration by promoting innervation, immunoregulation, vascularization, and osteogenesis in vivo. Moreover, the in vitro results further confirmed that this system significantly induced M2 polarization of macrophages, tube formation of HUVECs, and BMSCs osteogenic differentiation. Furthermore, BMSCs osteogenesis was promoted by upregulating the TGF-β1/SMAD2/3 signaling pathway. In summary, a novel cell-free and easily prepared SC Exo neural engineering was successfully developed to promote bone regeneration by orchestrating the entire bone healing microenvironment, which may provide a new strategy for tissue engineering and clinical treatment of bone defects.
Immune biomarkers of response to immunotherapy in patients with high-risk smoldering myeloma
Authors: Romanos Sklavenitis-Pistofidis, Michelle P. Aranha, Robert A. Redd, Joanna Baginska, Nicholas J. Haradhvala, Margaret Hallisey, Ankit K. Dutta, Alexandra Savell, Shohreh Varmeh, Daniel Heilpern-Mallory, Sylvia Ujwary, Oksana Zavidij, Francois Aguet, Nang K. Su, Elizabeth D. Lightbody, Mark Bustoros, Sabrin Tahri, Tarek H. Mouhieddine, Ting Wu, Lea Flechon, Shankara Anand, Jacalyn M. Rosenblatt, Jeffrey Zonder, James J. Vredenburgh, Adam Boruchov, Manisha Bhutani, Saad Z. Usmani, Jeffrey Matous, Andrew J. Yee, Andrzej Jakubowiak, Jacob Laubach, Salomon Manier, Omar Nadeem, Paul Richardson, Ashraf Z. Badros, Maria-Victoria Mateos, Lorenzo Trippa, Gad Getz, Irene M. Ghobrial
Journal: Cancer Cell (2022)
Diagnostic Optic Nerve Features in Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay
Authors: Jenny L. Hepschke, Yusuf Ali Rajabally, Susan P. Mollan
Journal: JAMA Neurology (2022)

This case report describes the optic nerve features of a male patient aged 23 years with a diagnosis of autosomal recessive spastic ataxia of Charlevoix-Saguenay.
Hyaluronan Receptors as Mediators and Modulators of the Tumor Microenvironment
Authors: Ana M. Carvalho, Rui L. Reis, Iva Pashkuleva
Journal: Advanced Healthcare Materials (2022)

Abstract The tumor microenvironment (TME) is a dynamic and complex matter shaped by heterogenous cancer and cancer‐associated cells present at the tumor site. Hyaluronan (HA) is a major TME component that plays pro‐tumorigenic and carcinogenic functions. These functions are mediated by different hyaladherins expressed by cancer and tumor‐associated cells triggering downstream signaling pathways that determine cell fate and contribute to TME progression toward a carcinogenic state. Here, the interaction of HA is reviewed with several cell‐surface hyaladherins—CD44, RHAMM, TLR2 and 4, LYVE‐1, HARE, and layilin. The signaling pathways activated by these interactions and the respective response of different cell populations within the TME, and the modulation of the TME, are discussed. Potential cancer therapies via targeting these interactions are also briefly discussed.
Circulating Exosomal PD-L1 at Initial Diagnosis Predicts Outcome and Survival of Patients with Osteosarcoma
Authors: Jun Wang, Wei Guo, Xiaofang Wang, Xiaodong Tang, Xin Sun, Tingting Ren
Journal: Clinical Cancer Research (2022)

Abstract Purpose: It is difficult to predict prognosis of patients with osteosarcoma at initial diagnosis due to lack of efficient prognostic parameters. We evaluated the relationship between level of circulating serum exosomal PD-L1 (Sr-exosomal PD-L1) at initial diagnosis and oncologic outcome during the follow-up. Experimental Design: Sixty-seven patients with newly diagnosed osteosarcoma were prospectively recruited. Fasting blood was collected and exosome isolation was performed using ultracentrifugation method. Evaluation of Sr-exosomal PD-L1 was performed respectively by immunogold labeling and ELISA method. Correlation between level of Sr-exosomal PD-L1 at initial diagnosis and clinical risk factors was assessed. Results: Mean follow-up was 46.7 months. Two-year and 5-year overall survival (OS) rates were respectively 96.9% and 62.5%. Two-year and 5-year disease-free survival (DFS) rates were respectively 85.0% and 31.4%. Results revealed a significantly positive association between high PD-L1 cargo of circulating exosomes and clinicopathologic disease markers such as pulmonary metastasis, multiple metastasis, and death. Patients who died of disease at final follow-up had higher level of Sr-exosomal PD-L1 at initial diagnosis, which compared with patients who were still alive at last follow-up. Patients in group of ≥14.23 pg/mL Sr-exosomal PD-L1 at initial diagnosis had inferior DFS compared with patients in group of &amp;lt;14.23 pg/mL at initial diagnosis. Patients in group of ≥25.96 pg/mL at initial diagnosis had poor OS compared with patients in group of &amp;lt;25.96 pg/mL at initial diagnosis. Conclusions: Use of liquid biopsy of circulating exosomal PD-L1 at initial diagnosis provides a robust means of predicting prognosis for patients with a newly diagnosed osteosarcoma.
Physical Activity and Rising Neurofilament Light Chain in Genetic Frontotemporal Degeneration—Diagnosis Is Not Destiny
Authors: Lauren Massimo, Katheryn A. Q. Cousins
Journal: JAMA Neurology (2022)

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Hydrogel Microtumor Arrays to Evaluate Nanotherapeutics
Authors: Yiling Liu, Stephanie Nemec, Chantal Kopecky, Martina H. Stenzel, Kristopher A. Kilian
Journal: Advanced Healthcare Materials (2022)

Nanoparticle drug formulations have many advantages for cancer therapy due to benefits in targeting selectivity, lack of systemic toxicity, and increased drug concentration in the tumor microenvironment after delivery. However, the promise of nanomedicine is limited by preclinical models that fail to accurately assess new drugs before entering human trials. In this work a new approach to testing nanomedicine using a microtumor array formed through hydrogel micropatterning is demonstrated. This technique allows partitioning of heterogeneous cell states within a geometric pattern-where boundary regions of curvature prime the stem cell-like fraction-allowing to simultaneously probe drug uptake and efficacy in different cancer cell fractions with high reproducibility. Using melanoma cells of different metastatic potential, a relationship between stem fraction and nanoparticle uptake is discovered. Deformation cytometry reveals that the stem cell-like population exhibits a more mechanically deformable cell membrane. Since the stem fraction in a tumor is implicated in drug resistance, recurrence, and metastasis, the findings suggest that nanoparticle drug formulations are well suited for targeting this dangerous cell population in cancer therapy.
Dual‐Responsive Nanocomposites for Synergistic Antibacterial Therapies Facilitating Bacteria‐Infected Wound Healing
Authors: Shi Cheng, Manlin Qi, Wen Li, Wenyue Sun, Meiqi Li, Jinying Lin, Xue Bai, Yue Sun, Biao Dong, Lin Wang
Journal: Advanced Healthcare Materials (2022)

Abstract The rising dangers of bacterial infections have created an urgent need for the development of a new generation of antibacterial technologies and therapeutics. Antibacterial photodynamic therapy (PDT), considered as a noninvasive treatment with no drug resistance, has become a new promising photochemistry‐involved treatment strategy. Titanium oxide (TiO 2 ) is proved to be a very efficient PDT agent among the photosensitive materials, while the property of a large bandgap of TiO 2 makes it only be excited by ultraviolet light, which is harmful to organisms. In this work, a novel ligand‐to‐metal charge transfer (LMCT) mediated TiO 2 PDT strategy is proposed via the harmless near‐infrared light irradiation. By choosing a mussel‐inspired material, polydopamine (PDA) is involved in forming mesoporous TiO 2 @PDA nanoparticles (mTiO 2 @PDA NPs). The catechol groups of PDA can attach the TiO 2 tightly even in colloidal environments, and can also form the LMCT bridge, exciting TiO 2 to exert PDT function via 808 nm irradiation. Combining the sonodynamic therapy (SDT) of TiO 2 and the photothermal therapy properties of PDA, this simple structure mTiO 2 @PDA enables synergistic antibacterial applications with multiple functions under the dual excitation of NIR and ultrasound. This reliable all‐in‐one NPs can achieve great antibacterial effect and a rapid repair of infected wounds.
Short-Course vs Long-Course Antibiotic Therapy for Children With Nonsevere Community-Acquired Pneumonia
Authors: Qinyuan Li, Qi Zhou, Ivan D. Florez, Joseph L. Mathew, Lianhan Shang, Guangli Zhang, Xiaoyin Tian, Zhou Fu, Enmei Liu, Zhengxiu Luo, Yaolong Chen
Journal: JAMA Pediatrics (2022)

Importance Short-course antibiotic therapy could enhance adherence and reduce adverse drug effects and costs. However, based on sparse evidence, most guidelines recommend a longer course of antibiotics for nonsevere childhood community-acquired pneumonia (CAP). Objective To determine whether a shorter course of antibiotics was noninferior to a longer course for childhood nonsevere CAP. Data Sources MEDLINE, Embase, Web of Science, the Cochrane Library, and 3 Chinese databases from inception to March 31, 2022, as well as clinical trial registries and Google.com. Study Selection Randomized clinical trials comparing a shorter- vs longer-course therapy using the same oral antibiotic for children with nonsevere CAP were included. Data Extraction and Synthesis Random-effects models were used to pool the data, which were analyzed from April 15, 2022, to May 15, 2022. Grading of Recommendations Assessment, Development and Evaluation (GRADE) was used to rate the quality of the evidence. Main Outcomes and Measures Treatment failure, defined by persistence of pneumonia or the new appearance of any general danger signs of CAP (eg, lethargy, unconsciousness, seizures, or inability to drink), elevated temperature (&amp;amp;gt;38 °C) after completion of treatment, change of antibiotic, hospitalization, death, missing more than 3 study drug doses, loss to follow-up, or withdrawal of informed consent. Results Nine randomized clinical trials including 11 143 participants were included in this meta-analysis. A total of 98% of the participants were aged 2 to 59 months, and 58% were male. Eight studies with 10 662 patients reported treatment failure. Treatment failure occurred in 12.8% vs 12.6% of participants randomized to a shorter vs a longer course of antibiotics. High-quality evidence showed that a shorter course of oral antibiotic was noninferior to a longer course with respect to treatment failure for children with nonsevere CAP (risk ratio, 1.01; 95% CI, 0.92-1.11; risk difference, 0.00; 95% CI, –0.01 to 0.01; I 2 = 0%). A 3-day course of antibiotic treatment was noninferior to a 5-day course for the outcome of treatment failure (risk ratio, 1.01; 95% CI, 0.91-1.12; I 2 = 0%), and a 5-day course was noninferior to a 10-day course (risk ratio, 0.87; 95% CI, 0.50-1.53; I 2 = 0%). A shorter course of antibiotics was associated with fewer reports of gastroenteritis (risk ratio, 0.79; 95% CI, 0.66-0.95) and lower caregiver absenteeism (incident rate ratio, 0.74; 95% CI, 0.65-0.84). Conclusions and Relevance Results of this meta-analysis suggest that a shorter course of antibiotics was noninferior to a longer course in children aged 2 to 59 months with nonsevere CAP. Clinicians should consider prescribing a shorter course of antibiotics for the management of pediatric nonsevere CAP.
Selectively Targeting STAT3 Using a Small Molecule Inhibitor is a Potential Therapeutic Strategy for Pancreatic Cancer
Authors: Huang Chen, Wenbo Zhou, Aiwu Bian, Qiansen Zhang, Ying Miao, Xuan Yin, Jiangnan Ye, Shifen Xu, Chaowen Ti, Zhenliang Sun, Jianghua Zheng, Yihua Chen, Mingyao Liu, Zhengfang Yi
Journal: Clinical Cancer Research (2022)

Abstract Purpose: Pancreatic cancer is the worst prognosis among all human cancers, and novel effective treatments are urgently needed. Signal transducer and activator of transcription 3 (STAT3) has been demonstrated as a promising target for pancreatic cancer. Meanwhile, selectively targeted STAT3 with small molecule remains been challenging. Experimental Design: To specifically identify STAT3 inhibitors, more than 1.3 million compounds were screened by structure-based virtual screening and confirmed with the direct binding assay. The amino acid residues that WB436B bound to were verified by induced-fit molecular docking simulation, RosettaLigand computations, and site-directed mutagenesis. On-target effects of WB436B were examined by microscale thermophoresis, surface plasmon resonance, in vitro kinase assay, RNA sequencing, and selective cell growth inhibition assessment. In vivo studies were performed in four animal models to evaluate effects of WB436B on tumor growth and metastasis. Kaplan–Meier analyses were used to assess survival. Results: WB436B selectively bound to STAT3 over other STAT families protein, and in vitro antitumor activities were improved by 10 to 1,000 fold than the representative STAT3 inhibitors. WB436B selectively inhibits STAT3-Tyr705 phosphorylation, STAT3 target gene expression, and the viability of STAT3-dependent pancreatic cancer cells. WB436B significantly suppresses tumor growth and metastasis in vivo and prolongs survival of tumor-bearing mice. Mechanistic studies showed that WB436B have unique binding sites located in STAT3 Src homology 2 domain. Conclusions: Our work presents the first-in-class selective STAT3 inhibitor WB436B as a potential therapeutic candidate for the treatment of pancreatic cancer.